[BioC] pmStrand() in oligo (version...)

[De Bondt, An-7114 [PRDBE]]

Hi Ben,

> dir(system.file("extdata", package = "pd.mapping250k.sty"))
[1] "pd.mapping250k.sty.sqlite" "seqMat.rda"

Is this the output what it should be?

An


-----Original Message-----
From: Benilton Carvalho [mailto:bcarvalh at jhsph.edu]
Sent: Tuesday, 5 June 2007 8:34
To: De Bondt, An-7114 [PRDBE]
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] pmStrand() in oligo (version...)


That's strange An.

Could you please tell us what you get with:

dir(system.file("extdata", package = "pd.mapping250k.sty"))

I wonder if there was a problem when you installed the pd.mapping  
package, as it (v. 0.2.5) does contain the Ref file application is  
complaining about...

cheers,
b


On Jun 5, 2007, at 2:22 AM, De Bondt, An-7114 [PRDBE] wrote:

> Hi Ben,
>
> Here some extra info, hopefully useful to pinpoint the issue:
>
>> rmaSty <- snprma(fsetSty)
>      This may take a while.
>      Adjusting for sequence and fragment length....... done.
>      Normalizing...Error in readChar(con, 5) : cannot open the  
> connection
>      In addition: Warning message:
>      cannot open compressed file ''
>> traceback()
>      3: readChar(con, 5)
>      2: load(system.file("extdata", paste(annot, "Ref.rda", sep = ""),
>        package = annot))
>      1: snprma(fsetSty)
>> package.version("pd.mapping250k.sty")
>      [1] "0.2.5"
>
>
> Cheers,
> An
>
>
> -----Original Message-----
> From: Benilton Carvalho [mailto:bcarvalh at jhsph.edu]
> Sent: Monday, 4 June 2007 17:02
> To: De Bondt, An-7114 [PRDBE]
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] pmStrand() in oligo (version...)
>
>
> Hi An,
>
> that's problably R complaining a file that it didn't find. The
> strange thing is that I can't reproduce it here. Could you please
> forward me the results of traceback()?
>
> This would happen if, for example, oligo finds the old version of the
> pd.mapping250k.sty package.
>
> b
>
> On Jun 4, 2007, at 8:07 AM, De Bondt, An-7114 [PRDBE] wrote:
>
>> Hi Ben,
>>
>> When using oligo version 1.0.2-3, the pmStrand function indeed
>> works :-)
>> but the snprma function results in an error:
>>
>>      fsetSty <- read.celfiles(dir()[grep("S.CEL", dir())])
>>      rmaSty <- snprma(fsetSty)
>>
>> Normalizing...Error in readChar(con, 5) : cannot open the connection
>> In addition: Warning message:
>> cannot open compressed file
>>
>> How can I check which connection needs to be established?
>>
>> Thanks in advance for your help!
>> An
>>
>> -----Original Message-----
>> From: Benilton Carvalho [mailto:bcarvalh at jhsph.edu]
>> Sent: Friday, 1 June 2007 15:30
>> To: De Bondt, An-7114 [PRDBE]
>> Cc: bioconductor at stat.math.ethz.ch
>> Subject: Re: [BioC] pmStrand() in oligo (version...)
>>
>>
>> Hi An,
>>
>> I fixed that problem, thanks for the report.
>>
>> Also, regarding the .crlmm.regions packages, these are not anymore
>> required.
>>
>> If you use the following version instead (which should appear soon on
>> BioC), these problems should be taken care of:
>>
>> http://www.biostat.jhsph.edu/~bcarvalh/oligo_1.0.2-3.tar.gz
>>
>> Thank you,
>>
>> b
>>
>> On Jun 1, 2007, at 5:10 AM, De Bondt, An-7114 [PRDBE] wrote:
>>
>>> Dear useRs,
>>>
>>> I am looking into the raw data of the 500K SNP arrays and I would
>>> like to
>>> select the data from only one strand, sense OR antisense.  How
>>> could I do
>>> this?  Probably something like:
>>>
>>>      fsetSty <- read.celfiles(dir()[grep("S.CEL", dir())])
>>>      strand.sty <- pmStrand(get(annotation(fsetSty)))
>>>
>>> but the last command results in "Error: could not find function
>>> "pmStrand""
>>> although ?pmStrand is recognised and gives...
>>>
>>> Description:
>>>      Returns the strand information on SNP arrays for PM probes (0 -
>>>      sense / 1 - antisense).
>>> Usage:
>>>      pmStrand(object)
>>> Arguments:
>>>   object: 'AffySNPPDInfo' object
>>>
>>>
>>>
>>> Thanks in advance for your help!
>>> An
>>>
>>>
>>> 	[[alternative HTML version deleted]]
>>>
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